From: Charles Plessy Date: Sun, 21 Dec 2014 05:04:53 +0000 (+0900) Subject: Nettoyage. X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=2bcab614c6e98c3df10cad9d4ef48c42430c9a7f;p=source%2F.git Nettoyage. --- diff --git a/Haskell/refSeqIdSymbol.en.po b/Haskell/refSeqIdSymbol.en.po deleted file mode 100644 index 28ffb7a5..00000000 --- a/Haskell/refSeqIdSymbol.en.po +++ /dev/null @@ -1,469 +0,0 @@ -# SOME DESCRIPTIVE TITLE -# Copyright (C) YEAR Free Software Foundation, Inc. -# This file is distributed under the same license as the PACKAGE package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: PACKAGE VERSION\n" -"POT-Creation-Date: 2014-12-21 04:48+0000\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"Language: \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#. type: Content of:

-msgid "A RefSeq parser that outputs the gene symbol for each ID" -msgstr "" - -#. type: Content of:

-msgid "The goal" -msgstr "" - -#. type: Content of:

-msgid "" -"RefSeq is a database of " -"reference biological (DNA, RNA or protein) seqences made " -"by the National Center for Biological Information (NCBI, USA). In a project " -"at work we wanted to list for each entry in the RNA database the unique " -"version number of the entry and its gene symbol (a short human-readable " -"name)." -msgstr "" - -#. type: Content of:

-msgid "" -"This looked like an excellent excuse to practice Haskell... this is the first program I " -"wrote in that language. I did not yet manage to make it run fast enough " -"compared to a minimalistic strategy using shell commands." -msgstr "" - -#. type: Content of:

-msgid "" -"Here I describe the format that I want to parse, the Haskell program I " -"wrote, and the quick-and-dirty processing with shell commands." -msgstr "" - -#. type: Content of:

-msgid "The GenBank format" -msgstr "" - -#. type: Content of:

-msgid "" -"Human sequences can be downloaded from NCBI's FTP " -"site, in a structured format called GenBank. " -"RefSeq entries typically start like the following one." -msgstr "" - -#. type: Content of: 

-#, no-wrap
-msgid ""
-"LOCUS       NM_131041               1399 bp    mRNA    linear   VRT "
-"28-SEP-2014\n"
-"DEFINITION  Danio rerio neurogenin 1 (neurog1), mRNA.\n"
-"ACCESSION   NM_131041\n"
-"VERSION     NM_131041.1  GI:18859080\n"
-"KEYWORDS    RefSeq.\n"
-"SOURCE      Danio rerio (zebrafish)\n"
-"  ORGANISM  Danio rerio\n"
-"            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; "
-"Euteleostomi;\n"
-"            Actinopterygii; Neopterygii; Teleostei; Ostariophysi;\n"
-"            Cypriniformes; Cyprinidae; Danio."
-msgstr ""
-
-#. type: Content of: 

-msgid ""
-"The record is made of fields, which start with their name in upper case at "
-"the beginning of a line. Similarly to e-mail "
-"headers, a field in the GenBank format includes the next line if this "
-"line starts with a space. Fields can be nested by indentation, like for the "
-"ORGANISM field above."
-msgstr ""
-
-#. type: Content of: 

-msgid ""
-"In the VERSION field, the version number is the first element (NM_131041.1 "
-"in the example above)."
-msgstr ""
-
-#. type: Content of: 

-msgid ""
-"The gene symbol is contained in the FEATURE field. In the record "
-"NM_131041.1, it starts like the following."
-msgstr ""
-
-#. type: Content of: 
-#, no-wrap
-msgid ""
-"FEATURES             Location/Qualifiers\n"
-"     source          1..1399\n"
-"                     /organism="Danio rerio"\n"
-"                     /mol_type="mRNA"\n"
-"                     /db_xref="taxon:7955"\n"
-"                     /chromosome="14"\n"
-"                     /map="14"\n"
-"     gene            1..1399\n"
-"                     /gene="neurog1"\n"
-"                     /gene_synonym="cb260; chunp6899; neurod3; ngn1; "
-"ngr1;\n"
-"                     zNgn1"\n"
-"                     /note="neurogenin 1"\n"
-"                     /db_xref="GeneID:30239"\n"
-"                     /db_xref="ZFIN:ZDB-GENE-990415-174""
-msgstr ""
-
-#. type: Content of: 

-msgid ""
-"The FEATURES field also contains indented sub-fields, but their name is not "
-"restricted to upper-case characters. These subfields are structured: their "
-"value starts with sequence coordinates, followed by a list of keys and "
-"values, where each pair of keys and values is separated by spaces and a "
-"slash '/'."
-msgstr ""
-
-#. type: Content of: 

-msgid ""
-"Lastly, GenBank records are terminated by a line that contains exactly two "
-"slashes (//) and nothing else."
-msgstr ""
-
-#. type: Content of: 

-msgid "The program"
-msgstr ""
-
-#. type: Content of: 

-msgid ""
-"This whole file is written using literate "
-"Haskell. It can actually be compiled! In literate Haskell, everything is "
-"comment by default and the code is prefixed by '> '."
-msgstr ""
-
-#. type: Content of: 
-#, no-wrap
-msgid ""
-"import Text.Parsec\n"
-"import Text.Parsec.String\n"
-"import Data.List "
-"(intercalate)\n"
-"import Data.List.Split "
-"(splitOn)"
-msgstr ""
-
-#. type: Content of: 

-msgid ""
-"I used the Parsec "
-"package for parsing, as well as two helper functions from packages related "
-"to list handling."
-msgstr ""
-
-#. type: Content of: 
-#, no-wrap
-msgid ""
-"main = do\n"
-"  r <- getContents\n"
-"  let rs = splitOn "//\\n" r\n"
-"  mapM_ parseGbRecord rs"
-msgstr ""
-
-#. type: Content of: 

-msgid ""
-"It does not seem possible to parse a stream of text: the whole parsing must "
-"be finished before a result is returned, which was not feasable with "
-"hundreds of megabytes of data. Therefore, in the main loop getting the "
-"contents from stdin, I split the records one after the other, and "
-"run the parser on each of them."
-msgstr ""
-
-#. type: Content of: 
-#, no-wrap
-msgid ""
-"parseGbRecord "
-":: String -> "
-"IO ()\n"
-"parseGbRecord r = case "
-"parse gbRecord "(stdin)" r of\n"
-"            Left e  -> do putStrLn "Error parsing input:"\n"
-"                          print e\n"
-"            Right r ->  putStrLn r"
-msgstr ""
-
-#. type: Content of: 

-msgid "Parsec returns either an error message or the result of the parsing."
-msgstr ""
-
-#. type: Content of: 

-msgid ""
-"TODO: how about printing always ? What is the difference between pring and "
-"putStrLn ?"
-msgstr ""
-
-#. type: Content of: 
-#, no-wrap
-msgid ""
-"gbRecord = "
-"do\n"
-"  fs <- many field\n"
-"  return . intercalate "\\t" $ filter "
-"(/= "") "
-"fs"
-msgstr ""
-
-#. type: Content of: 

-msgid ""
-"A GenBank record is made of many fields. For each field the parser reports a "
-"string, so the result will be a list of strings. Some strings will be empty "
-"and discarded. The resulting list is collapsed in a tab-separated string."
-msgstr ""
-
-#. type: Content of: 
-#, no-wrap
-msgid ""
-"field = do\n"
-"  f <- fieldName\n"
-"  many1 space\n"
-"  case f of\n"
-"    "VERSION"  -> getVersionNumber\n"
-"    "FEATURES" -> getGeneSymbol\n"
-"    _          -> endField >> return """
-msgstr ""
-
-#. type: Content of: 

-msgid ""
-"A field starts with a field name, which is recorded. It is followed with "
-"multiple spaces. Since I am only intersted in version and gene symbol, if "
-"the field name was VERSION or FEATURES, more information is extracted, "
-"otherwise an empty string is returned."
-msgstr ""
-
-#. type: Content of: 
-#, no-wrap
-msgid ""
-"fieldName = "
-"many1 upper\n"
-"endField  = manyTill anyChar (try separator <|> try eof)\n"
-"separator = newline >> notFollowedBy (char ' "
-"')"
-msgstr ""
-
-#. type: Content of: 

-msgid ""
-"A field name is upper case. Fields continue with any character until a "
-"separator or the end of the file is reached. A separator is a newline "
-"character not followed by a space."
-msgstr ""
-
-#. type: Content of: 
-#, no-wrap
-msgid ""
-"getVersionNumber = do\n"
-"  let versionNumberChar = oneOf $ "NXRM_" ++ ['0'..'9'] ++ "."\n"
-"  v <- many versionNumberChar\n"
-"  endField\n"
-"  return v"
-msgstr ""
-
-#. type: Content of: 

-msgid ""
-"A version number is a string containing the letters N, X, R or M, "
-"underscores, digits and dots. The precise definition is actually stricter: "
-"the version numbers start by NM_, NR_, XM_ or XR_, but I was worried of the "
-"performance hit if testing for this precisely."
-msgstr ""
-
-#. type: Content of: 

-msgid ""
-"Once the version number is read, it is recorded, and the rest of the field "
-"is discarded."
-msgstr ""
-
-#. type: Content of: 
-#, no-wrap
-msgid ""
-"getGeneSymbol = "
-"do\n"
-"  let geneSymbolChar = "
-"oneOf $ ['A'..'Z'] ++ "orf" ++ "p" ++ "-" ++ ['0'..'9']\n"
-"  manyTill anyChar (try (string "/gene=\\""))\n"
-"  g <- many geneSymbolChar\n"
-"  char '"'\n"
-"  endField\n"
-"  return g"
-msgstr ""
-
-#. type: Content of: 

-msgid ""
-"Similarly, a gene symbol is made of uppercase letters, lower-case o, r, f or "
-"p, dashes and digits. It is recorded after finding the string "
-"/gene=". The parser then checks that the closing double "
-"quote is present, and discards it together with the rest of the field."
-msgstr ""
-
-#. type: Content of: 

-msgid "Quick-and-dirty parsing with Unix tools"
-msgstr ""
-
-#. type: Content of: 

-msgid ""
-"With the following command, I could produce a list of version numbers and "
-"gene symbols in a minute or so. However, what it does is not very obvious, "
-"nor flexible as it does not follow the format's syntax, and is probably very "
-"fragile."
-msgstr ""
-
-#. type: Content of: 
-#, no-wrap
-msgid ""
-"zcat human.*.rna.gbff.gz |\n"
-"  grep -e VERSION -e gene= |\n"
-"  uniq |\n"
-"  sed 's/=/ /' |\n"
-"  awk '{print $2}' |\n"
-"  tr '\\n' '\\t' |\n"
-"  sed -e 's/"\\t/\\n/g' -e 's/"//g' > "
-"human.rna.ID-Symbol.txt"
-msgstr ""
-
-#. type: Content of: 

-msgid "In brief, it:"
-msgstr ""
-
-#. type: Content of: 
  • 
-msgid ""
-"filters lines containing VERSION or gene= and "
-"discards the other ones;"
-msgstr ""
-
-#. type: Content of: 
    • 
-msgid ""
-"removes consecutive duplicates (there are multiple features per locus "
-"crosslinking to gene IDs), assuming that only one gene symbol is used per "
-"record;"
-msgstr ""
-
-#. type: Content of: 
      • 
-msgid ""
-"replaces = with a space so that the relevant information "
-"appears to be on the second column if one considers the flowing text to be a "
-"space-separated table;"
-msgstr ""
-
-#. type: Content of: 
        • 
-msgid ""
-"keeps only the second column (at that point, the version numbers and gene "
-"symbols alternate on successive lines;"
-msgstr ""
-
-#. type: Content of: 
          • 
-msgid ""
-"replaces newlines by tabulations, so that the data is now a gigantic lines "
-"where tab-separated fields alternate for version numbers and symbols;"
-msgstr ""
-
-#. type: Content of: 
            • 
-msgid ""
-"uses the double quotes around the gene symbol as a landmark to transform the "
-"flowing text into a tab-separated file with the two wanted fields;"
-msgstr ""
-
-#. type: Content of: 
              • 
-msgid "cleans up the remaining double quotes."
-msgstr ""
-
-#. type: Content of: 
                
-msgid "Speed"
-msgstr ""
-
-#. type: Content of: 
                
-msgid ""
-"Unfortunately, the Haskell version is way too slow to process the full "
-"RefSeq data. Here is a comparison using a test file of only 476 Kib."
-msgstr ""
-
-#. type: Content of: 
                -#, no-wrap
-msgid ""
-"$ ghc -O2 refSeqIdSymbol.lhs\n"
-"[1 of 1] Compiling Main             ( refSeqIdSymbol.lhs, refSeqIdSymbol.o "
-")\n"
-"Linking refSeqIdSymbol ...\n"
-"chouca⁅~⁆$ time ./refSeqIdSymbol < hopla.gb \n"
-"NM_001142483.1  NREP\n"
-"NM_001142481.1  NREP\n"
-"NM_001142480.1  NREP\n"
-"NM_001142477.1  NREP\n"
-"NM_001142475.1  NREP\n"
-"NM_001142474.1  NREP\n"
-"NM_004772.2 NREP\n"
-"NM_001142466.1  GPT2\n"
-"NM_133443.2 GPT2\n"
-"NM_173685.2 NSMCE2\n"
-"NM_007058.3 CAPN11\n"
-"\n"
-"\n"
-"real    0m0.701s\n"
-"user    0m0.664s\n"
-"sys 0m0.028s"
-msgstr ""
-
-#. type: Content of: 
                -#, no-wrap
-msgid ""
-"$ time cat hopla.gb | grep -e VERSION -e gene= |   uniq |   sed "
-"'s/=/ /' |   awk '{print $2}' |   tr '\\n' "
-"'\\t' |   sed -e 's/"\\t/\\n/g' -e "
-"'s/"//g'\n"
-"NM_001142483.1  NREP\n"
-"NM_001142481.1  NREP\n"
-"NM_001142480.1  NREP\n"
-"NM_001142477.1  NREP\n"
-"NM_001142475.1  NREP\n"
-"NM_001142474.1  NREP\n"
-"NM_004772.2 NREP\n"
-"NM_001142466.1  GPT2\n"
-"NM_133443.2 GPT2\n"
-"NM_173685.2 NSMCE2\n"
-"NM_007058.3 CAPN11\n"
-"\n"
-"real    0m0.015s\n"
-"user    0m0.004s\n"
-"sys 0m0.004s"
-msgstr ""
diff --git a/kunpuu/sources.en.po b/kunpuu/sources.en.po
deleted file mode 100644
index a62ac37e..00000000
--- a/kunpuu/sources.en.po
+++ /dev/null
@@ -1,23 +0,0 @@
-# SOME DESCRIPTIVE TITLE
-# Copyright (C) YEAR Free Software Foundation, Inc.
-# This file is distributed under the same license as the PACKAGE package.
-# FIRST AUTHOR , YEAR.
-#
-#, fuzzy
-msgid ""
-msgstr ""
-"Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2014-12-21 04:48+0000\n"
-"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
-"Last-Translator: FULL NAME \n"
-"Language-Team: LANGUAGE \n"
-"Language: \n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-
-#. type: Content of: outside any tag (error?)
-msgid ""
-"http://photo.charles.plessy.org/kunpuu"
-msgstr ""
diff --git a/kunpuu/sources.html b/kunpuu/sources.html
deleted file mode 100644
index 6af2573c..00000000
--- a/kunpuu/sources.html
+++ /dev/null
@@ -1 +0,0 @@
-http://photo.charles.plessy.org/kunpuu